26 Apr

May 10th, 2019 – Guest Speaker: Benedikt Beckmann

Mark your calendars! On May 10th at 10a.m. in room VKL 5.1.31, Benedikt Beckmann will talk about novel methods to study RNA-protein interactions during bacterial infection (click here for the advert). Benedikt is a group leader at the Integrated Research Institute (IRI) for the Life Sciences in Berlin, an institute shared between the Humboldt University Berlin, the Charité University Clinic and the Max-Delbrück-Center for Molecular Medicine.

His research focuses on RNA-protein interactions in host cells during infection by pathogenic bacteria which he studies by employing classical molecular biology methods in combination with systems biology approaches and bioinformatics. Using Salmonella typhimurium as a model system, he investigates whether bacterial-derived non-coding RNAs and RNA-binding proteins can directly manipulate host cell gene expression on a post-transcriptional level e.g. to manipulate the immune repsponse of the host.

Recently, Bene established a novel methodological approach to generate RNA interactomes by employing organic extraction for the purification of UV cross-linked ribonucleoproteins (PTex). Previous methods relied on oligo-dT oligonucleotides to capture cross-linked RNPs by hybridization to the poly(A)-tail, limiting their applicability to eukaryotic organisms. Furthermore, Bene will talk about a recently developed machine learning-based tool for the de novo prediction of RNA-binding proteins across a wide variety of species (TriPepSVM).

 

18 Feb

2nd Regensburg – Canberra Symposium on RNP Biology

On February 14th and 15th, the second Regensburg – Canberra Symposium on RNP Biology took place at the John Curtin School of Medical Research at the Australian National University (ANU) in Canberra with the aim to further strengthen our collaborations and to pave the way for establishment of an international PhD program. It was great to meet down under and to hear about the exciting research on RNA biology at the ANU.

I would like to thank our colleagues in Canberra very much for organization of this wonderful meeting and for their generous hospitality.

John Curtin School of Medical Research at the Australian National University

25 Jan

How to stabilize a sex-specific gene expression pattern in male flies

New manuscript from the lab published in Nucleic Acids Research: Drosophila Sister-of-Sex-lethal reinforces a male-specific gene expression pattern by controlling Sex-lethal alternative splicing.

In a collboration with the labs of Stefan Schneuwly, Gunter Meister (both at the University of Regensburg), Michael Krahn (Westfälische Wilhelms-Universität Münster), and Oliver Rossbach (Justus-Liebig-University Giessen), we could demonstrate that the protein Sister-of-sex-lethal (Ssx) is required in male flies to suppress production of Sex-lethal (Sxl).

 

Genomic tagging of the Sex-lethal (Sxl) locus in flies to reveal Sxl protein mis-expression (arrowheads) in male flies mutant for Sister-of-Sex-lethal. Arrows mark expression of a Sxl isoform in neural cell bodies and projections.

 

Most higher eukaryotes reproduce sexually, increasing the variability in the offspring. This allows e.g. rapid adaption to a new (or changing) environment or the cleansing of harmful mutations from a population. Sexual reproduction in higher eukaryotes usually involves individuals of different sex: males and females. Not surprisingly, the genetic programs that determine sex and control sexual differentiation need to be particularly robust in order to ensure survival of the population.

In Drosophila, a single protein, the master regulator Sex-lethal (Sxl), governs female development by controlling the expression of key factors involved in female morphology and behaviour. Once expressed, it engages in an auto-regulatory, positive feedback loop to ensure its sustained expression. This stably ‘flips the switch’ and commits to female development.

In contrast, in males Sxl expression needs to be shut-off which is achieved by alternative splicing that generates RNA isoforms encoding truncated, non-functional Sxl protein. Fluctuations inherent to gene expression can, however, produce small amounts of functional Sxl protein. When left unchallenged, this protein can trigger a self-enforcing cascade resulting in Sxl protein expression snowballing out of control. Until now, however, it remained unclear how males completely shut off the Sxl expression cascade and protect themselves against runaway protein production to ensure robust sex-specific development.

We have discovered a safeguard mechanism that prevents Sxl production in adult male flies. We identified the protein Sister of Sex-lethal (Ssx) as the first antagonist of Sxl-mediated auto-regulatory splicing that defines a precise threshold level for activation of the auto-regulatory, positive feedback loop that controls Sxl expression. We could show that Ssx exerts function by competing with Sxl for the same RNA regulatory elements thus preventing Sxl from triggering the self-enforcing expression cascade in adult male animals.

 

1 Nov

Methods course on RNP analyses – from ensembles to single molecules

From October 8th to 10th 2018, a hands-on methods course took place at the University of Regensburg, aimed at training PhD students in the latest methods of ribonucleoprotein (RNP) analysis. Topics included the quantification of protein-RNA interactions, single molecule analyses of RNPs by fluorescence resonance energy transfer (FRET) or fluorescence in situ hybridization (FISH), RNA structure probing, and comprehensive capture of RNA-binding proteins by interactome profiling from cultured cells. The course attracted PhD students from labs around the globe, some travelling from as far as Canberra, Australia, to get insight in and training on a variety of biophysical and biochemical methods. The design of the course was also aimed at fostering interactions between the participants, allowing them to build networks with peers working on related topics. Besides the lectures and the practical hands-on training, it was particularly the vivid and intense discussions among the participants that made this course a big success.

We are extremely grateful for the support of many expert speakers and trainers that delivered lectures on the latest methodological developments and that supervised the experimental work. In particular we want to thank the invited speakers from industry and academia that travelled to Regensburg to provide expert guidance: Rastislav Horos (European Molecular Biology Laboratory, EMBL, Heidelberg), Agatha Korytowski (Malvern Panalytical), Stefanie Nunes Rosa (Swedish University of Agricultural Sciences, Uppsala), Joel Perez-Perri (EMBL Heidelberg), Bruno Sargueil (CNRS/Paris Descartes University), and Ralf Seidel (Peter Debye Institute for Soft Matter Physics, Universität Leipzig).

The course was organized by the Graduate Research Academy RNA Biology of the Collaborative Research Centre 960 (SFB960, Ribosome formation: principles of RNP biogenesis and control of their function) that also provided financial support.

picture courtesy of Kinga Ay

16 Oct

Honorary Doctorate for Thomas Cech

A particular highlight is coming up next week: Prof Thomas Cech will be awarded a honorary doctorate by the University of Regensburg. Tom Cech, now Professor at the University of Colorado at Boulder and director of the BioFrontiers Institute, was awarded the Nobel Prize in chemistry in 1989 jointly with Sidney Altman for the discovery of the catalytic activity of RNA. His revolutionary discovery of self-splicing in Tetrahymena thermophila radically changed the way we were thinking about RNA – what was previously considered a mere carrier of genetic information turned out to play the key function in fundamental biological processes. Exemplarily, protein synthesis is catalyzed by the RNA moiety of the large ribosomal subunit which promotes the peptidyl transfer reaction by which peptide bonds are formed between amino acids. His discovery also had a huge impact on my own scientific career and convinced me that RNA is the most interesting biomolecule to study. I am very much looking forward to the Symposium on Monday, October 22nd (starting 3:30p.m. in lecture hall H51) and to finally get the opportunity to meet Tom Cech in person!

4 Oct

Annual Conference of the Giessen Graduate Centre for the Life Sciences (GGL)

It was a particular honor to be invited by the students of the International Giessen Graduate Centre for the Life Sciences (GGL) to deliver a keynote lecture during the annual conference which ieatures an exciting and diverse program covering ten interdisciplinary research sections. The two days were packed with fascinating talks covering diverse topics ranging from ecology and bioresources to reproduction, cardiovascular disease, immunity and metabolism.

Apart from the great conference, it was particularly nice to return to my Alma Mater – the Justus-Liebig-Universität Giessen – and to catch up with old friends and colleagues in the various departments. Also, I was very impressed by the new buildings (on and close to the life science campus) – an extraordinary demonstration of how well the University is developing and growing.

I would like to thank the students of the ‘Protein and Nucleic Acid Interactions’ section of the GGL very much for the kind invitation and the entire GGL team for the hospitality!

Picture courtesy of Dr. L. Lück, managing director of the GGL

2 Oct

From Ensembles to Single-Molecule Analysis

Mark your calendars! From October 8th to 12th the Graduate Research Academy RNA Biology of the Collaborative Research Center 960 (SFB960 – Ribosome formation: principles of RNP biogenesis and control of their function) is hosting a practical course on modern methods for the analysis of ribonucleoproteins (RNPs). Diverse topics will be covered ranging from biophysical analyses (such as isothermal calorimetry and thermophoresis), single-molecule RNP studies (single-molecule FRET and FISH), RNA structure probing and the latest RNA interactome capture methodology. In the morning, renowned experts will deliver lectures to introduce the individual topics, followed by hands-on experimentation in the afternoon. All lectures are open to the public, so even if you didn’t register, you certainly don’t want to miss out on the exciting talks by Rastislav Horos (EMBL Heidelberg), Agatha Korytowski (Malvern Panalytical GmbH), Stefanie Nunes Rosa (Swedish University of Agricultural Sciences, Uppsala), Joel Perez-Perri (EMBL Heidelberg), Bruno Sargueil (CNRS/ Paris Descartes University), and Ralf Seidel (Universität Leipzig)!

 

 

2 Sep

Understanding RNA-based Regulation in Cells

It was a particular honor to be invited for the PhD choice lecture to the conference of the Collaborative Research Center 902 – Molecular Principles of RNA-based Regulation which took place on August 29th and 30th 2018 at the Otto-Stern-Zentrum in Frankfurt am Main. The conference featured many exciting talks on diverse topics in RNA biology.

I would like to thank the PhD students very much for the invitation – it was a real pleasure to participate in the conference!

8 Jun

NEW FINDING: Purification of Cross-linked RNA-Protein Complexes by Organic Extraction

The advent of interactome capture has allowed the unbiased identification of RNA binding proteins (RBPs) dramatically expanding their number and yielding novel insights into RNA biology (see also our recent review).

For interactome capture, RBPs are photo-cross-linked to their RNA targets. Subsequently, oligo-dT resin is used to capture polyadenylated RNAs and to co-purify with them the covalently bound proteins. RNAs that lack a ploy(A)-tail can, however, not be captured by this approach, limiting its broad application. In particular, prokaryotic organisms that do not polyadenylate their mRNAs are not amenable to interactome capture.

Now three manuscripts have been uploaded to bioRxiv by the Lilley, Krijgsveld, and Beckmann labs (we contributed to one of them). In all cases extraction with organic solvents is employed to purify cross-linked RNPs (see figure) circumventing the requirement of a poly(A)-sequence for RNP capture. Moreover, this approach also captures RBPs that bind to RNA as short as 30 nt.

 

 

The manuscripts can be found here:

Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction

Unbiased dynamic characterization of RNA-protein interactions by OOPS

The Human RNA-Binding Proteome and Its Dynamics During Arsenite-Induced Translational Arrest

12 Apr

RNA Transport Meeting 2018

Organized and hosted by the DFG-funded Research Unit 2333 ‘Macromolecular complexes in mRNA localization’ (FOR2333), the RNA transport meeting 2018 took place from March 3rd to 6th in Düsseldorf. The keynote lectures by Christine Mayr and Erin Schuman were embedded in an exciting scientific program that featured talks by 18 invited speakers and by members of the FOR2333 network. For us it was a great opportunity to share and discuss our latest findings with the community.

1 Dec

Good News: Jan’s Habilitation is almost finished…

On Wednesday, November 29th, Jan successfully finished the final phase of his Habilitation by delivering a lecture in front of the entire faculty.

`I want to thank everybody who supported me along the way, in particular my lab and the colleagues in the Biochemistry I department of the University of Regensburg, especially Gunter Meister. Also without the help of our colleagues in the Collaborative Research Center 960 (Sonderforschungsbereich SFB960), our excellent collaborators, and the funding (provided by BioSysNet, DFG and BMBF) we would not have succeeded with our scientific work that was an essential part of the Habilitation.´

It is a german tradition to prepare a handcrafted hat as a present for candidates that have just obtained their doctoral degree. Jan also got a super-cool Drosophila hat for his Habilitation – thank you to everybody who helped crafting it!

29 Nov

Another manuscript accepted…

Nucleic Acids Research just accepted another manuscript for publication to which we have contributed. In an experimental effort headed by our colleague Sébastien Ferreira-Cerca (University of Regensburg, Biochemistry III), the function of the atypical Rio kinases in ribosomal smal subunit (SSU) biogenesis and maturation was addressed in Archea. This revealed activation of Rio2 by an ancient and conserved mechanism involving ribosomal RNA that stimulates release of the kinase from the nascent 40S particle. Watch out for the next NAR table of contents: there you should find a link to the manuscript, once it is out!

16 Nov

RNA transport meeting coming up…

picture courtsey of M. Feldbrügge

Registration is now open for the RNA transport meeting 2018, hosted by the Forschergruppe2333! The Conference will take place from March 3rd to 6th, 2018 in Düsseldorf. It features a great line-up of invited speakers and aims to bring together various experts from a broad field of RNA biology with the goal of representing the current state of the mRNA-localization field. It’s going to be a really exciting meeting – you don’t want to miss out on that, so make sure to register soon!

10 Nov

Sino-German Symposium on RNA Biology

 

The second Sino-German Symposium on RNA Biology with the title `From Big Data and Structure to Novel Mechanisms´ was held in Shanghai from November 4th to 8th. It was an exceptional meeting featuring many scientific highlights!

The meeting was co-organized by the CAS-MPG Partner Institute for Computational Biology (co-established by the Chinese Academy of Sciences and the Max Planck Society) and the CAS Key Laboratory of Computational Biology. I want to thank our hosts for their outstanding hospitality and the great organization. It was a truly outstanding combination of state-of-the-art science with cultural and culinary highlights in the vibrant city of Shanghai. Xièxiè to all of you!